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XenA Y183F variant in complex with ethyl (Z)-2-(hydroxyimino)-3-oxobutanoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N19
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293.15 100 mM (Tris (base); BICINE) pH 8.5; 30 mM Magnesium chloride hexahydrate; 30 mM Calcium chloride dihydrate; 12,5% v/v MPD; 12,5% PEG 1000; 12,5% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.32 46.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.07 α = 90 b = 157.63 β = 90 c = 57.34 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 X 16M 2021-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03319 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.35 46.37 98.95 0.998 11.08 3.5 317934 13.85
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.351 1.4 0.661
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3n19 1.35 46.37 1.36 165324 2099 98.95 0.1571 0.1569 0.159 0.173 0.1751 18.97
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.4344 f_angle_d 0.8569 f_chiral_restr 0.0758 f_plane_restr 0.0062 f_bond_d 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5618 Nucleic Acid Atoms Solvent Atoms 866 Heterogen Atoms 128
Software Software Software Name Purpose PHENIX refinement PHASER phasing Aimless data scaling XDS data reduction AutoProcess data processing